As your finding, shooting a pistol accurately is more difficult than shooting long arms.
Slight errors that don't effect rifle shooting much show up all too easily with a pistol.
A right handed shooter who's pistol shots are hitting above the point of aim often indicates the shooter is "pushing" or "heeling" the grip in anticipation of the shot.
Here is a link which shows some shooting errors common to pistol shooting:
http://www.firearmstalk.com/forums/f55/proper-sight-picture-target-mistakes-4871/
Sighting errors are also easy to make so my recommendations for pistol shooting are:
Maintain a firm but not overly firm (tight) grip on the gun.
Some people get a death grip on a pistol but that is unnecessary. The recoil is not going to cause the gun to slip or jump out of the shooters hand.
Keep your aiming eye on the front sight and its alignment with the rear sight.
The target will look fuzzy but only by watching the sights can the shooter know where the gun is actually aimed.
The sights will never align and hold exactly on the center of the target. It is humanly impossible to hold the gun that steady.
Some are really bothered by this but a good shooter will watch as the target moves but keep his concentration only on the center of the target.
Squeeze the trigger slowly and smoothly.
Some people jerk or slap the pistol. Any sudden movement of a finger or the hand will result in a missed shot.
This jerking of the trigger is often a result of trying to get the gun to fire as the sights are passing by the center of the bullseye. It always results in a poor shot.
Do not try to anticipate when the shot will happen. Just let the gun do its thing.
It's easy to unconsciously stiffen up or to push against the recoil of the gun. This will always ruin the shot.
It's equally easy to forget to follow thru after the shot.
Following thru is important because your senses cannot really determine where the bullet is and any movement while it is still in the barrel will result in a poor shot.
When I used to shoot in competition I would position my body relative to the target.
Then making sure the pistol was held so it felt like an extension of my arm I would begin to raise the pistol towards the target while taking in a deep breath.
As the gun was being aligned with the target I would let out about half of my breath as my eye focused on the front sight.
With the pistol aligned with the target I would concentrate only on the sight and its alignment with the point on the target I wanted to hit. (I did not like the 6:00 o'clock hold).
As the sight aligned I would begin to tighten my trigger finger, still with all of my concentration on the front sight and the target.
I really never knew when the gun would fire but as it did I continued to hold my arm in alignment with the target even though the gun was recoiling.
Only after the gun had finished recoiling and had started back down towards the target would I relax my arm and allow the gun to point down below the target.
Others may use a different method and as long as it's working for them that's fine and dandy but my method worked for me. (Until my eyes started going bad).